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Wei-Chen CHU, Ph.D.

Weichen-photo

Profile

  • I'm an Imaging Core Facility Manager and Bioimage Analyst passionate about empowering researchers to generate high-quality imaging data and develop reproducible analysis workflows. I teach confocal microscopy and bioimage analysis with FIJI and AI tools, equipping trainees with the skills to independently plan, acquire, and troubleshoot their experiments. As part of my commitment to open science, I develop and share open-access training materials. Beyond training, I design and implement custom bioimage analysis workflows and provide expert consultation for advanced imaging projects.
  • If you’re interested in collaboration, or consulting on bioimaging analysis projects, I’d love to connect.🙂

Professional Experience

  • Imaging Core Facility, Institute of Cellular and Organismic Biology (ICOB), Academia Sinica, Taiwan

    • R&D Scientist (Jan 2024 - Present)
    • Project Scientist (Oct 2021 - Dec 2023)
    • Research Technical Employee (Sep 2021)
    • Postdocroal Researcher (May 2021- Aug 2021)

  • RIKEN Center for Biosystems Dynamics Research (BDR), Japan

    • Research Scientist (Sep 2017 - Mar 2021)
    • Visiting Scientist (Oct 2016 - Sep 2017)
      Supported by Postdoctoral Research Abroad Program, Ministry of Science and Technology, Taiwan
    • Research Scientist (Jul 2015 - Sep 2016)

Education

  • Ph.D., Life Science
    Graduate Institute of Life Science, National Defense Medical Center, Taiwan
  • Master's, Life Science
    Department of Life Science, National Chung Hsing University, Taiwan
  • Bachelor's, Life Science
    Department of Life Science, National Chung Hsing University, Taiwan

Core Skills

  • Confocal Microscopy/ Fluorescence microscopy
  • Immunofluorescence, fluorescence protein tagging
  • Bio-Image processing and analysis using FIJI/ ImageJ, Napari and Imaris
  • GPU-accelerated image processing libraries (CLIJ series in FIJI, clEsperanto in Python)
  • Developing custom image processing and analysis workflows using ImageJ Macro or Python

Honors & Awards

  • Outstanding Employee 2024, Academia Sinica, Taiwan
    (113年中央研究院工作績優人員)
  • Drosophila Image Award 2022: Honorable Mention
  • RIKEN Incentive Project FY2018
  • Postdoctoral Research Abroad Program 2016, Ministry of Science and Technology, Taiwan

Membership Affiliations

Organizing Bioimage Analysis Traing Course

Attended Bioimaing and Bioimage Analysis Training Course

Open-Access Training Materials

Open-Source Bioimaging Analysis Workflows / Tools

  • LLSM-Batch-Preprocessing
    This repository contains customized ImageJ/Fiji macros designed for the preprocessing of large-volume Light-Sheet Microscopy raw image data. These scripts utilize GPU-accelerated processing to suppress background noise, enhance the cellular nuclei signal-to-noise ratio (SNR) for spot detection, and smooth structural boundaries for anatomical segmentation, preparing the data for downstream quantification in Imaris.

  • yeast-nuclear-puncta-cell-counter
    A image analysis pipeline for automated detection and quantification of nuclear puncta in yeast fluorescence microscopy images.

  • TF-Nuclear-Translocation-Analysis
    This repository provides Python scripts for refining single-cell trajectories and quantitatively measuring stress-induced nuclear translocation of the Dot6–GFP transcription factor from time-lapse microscopy data. The scripts operate after image acquisition, segmentation, and tracking, which are assumed to be performed in Fiji/ImageJ with Trackmate-Cellpose.

  • TIRF_vesicle_colocalize_analysis
    This repository contains Python code for analyzing time series TIRF (Total Internal Reflection Fluorescence) microscopy images to identify and track colocalized Glut10 and Rab5 vesicles.

  • Cell_Dist_Mesh_Generator
    This repository hosts a FIJI/ImageJ macro tailored for the automated generation of distance meshes between cells, aiding in quantitative visualization.

  • central-nuclei-muscle-analyzer
    A comprehensive ImageJ macro for automated analysis of nuclear localization in muscle cross-sectional areas, specifically designed to identify and quantify central nuclei in muscle fibers.

  • IJ_Hot_LUTs_palette
    This repository provides color palettes (.pal files) for Imaris, with a special focus on the popular "Hot" series of Look-Up Tables (LUTs) from ImageJ/Fiji. These LUTs are excellent for visualization.

Invited Talk

Publications